P06839

PR
Gene name
RAD3 (REM1, YER171W)
Protein name
General transcription and DNA repair factor IIH helicase subunit XPD
Names
TFIIH subunit XPD, DNA repair helicase RAD3, RNA polymerase II transcription factor B subunit RAD3, TFB subunit RAD3
Species
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast)
KEGG Pathway
sce:YER171W
EC number
3.6.4.12: Acting on ATP; involved in cellular and subcellular movement
Protein Class

Descriptions

The autoinhibited protein was predicted that may have potential autoinhibitory elements via cis-regPred.

Autoinhibitory domains (AIDs)

702-778 (Predicted disordered autoinhibitory region) PR

Target domain

Relief mechanism

Assay

cis-regPred

Accessory elements

No accessory elements

References

Autoinhibited structure

Activated structure

26 structures for P06839

Entry ID Method Resolution Chain Position Source
5FMF EM 600 A Y 1-778 PDB
5OQJ EM 470 A 0 1-778 PDB
5OQM EM 580 A 0 1-778 PDB
5SVA EM 1530 A Y 1-778 PDB
6GYM EM 670 A 0 1-778 PDB
7K01 EM 390 A 0 1-778 PDB
7K04 EM 925 A 0 1-778 PDB
7M2U EM 820 A 0 1-778 PDB
7ML0 EM 300 A 0 1-778 PDB
7ML1 EM 400 A 0 1-778 PDB
7ML2 EM 340 A 0 1-778 PDB
7ML3 EM 760 A 0 1-778 PDB
7ML4 EM 310 A 0 1-778 PDB
7O4I EM 320 A 0 1-778 PDB
7O4J EM 290 A 0 1-778 PDB
7O4K EM 360 A 0 1-778 PDB
7O4L EM 340 A 0 1-778 PDB
7O72 EM 340 A 0 1-778 PDB
7O73 EM 340 A 0 1-778 PDB
7O75 EM 320 A 0 1-778 PDB
7ZS9 EM 310 A 0 1-778 PDB
7ZSA EM 400 A 0 1-778 PDB
7ZSB EM 660 A 0 1-778 PDB
8CEN EM 300 A 0 1-778 PDB
8CEO EM 360 A 0 1-778 PDB
AF-P06839-F1 Predicted AlphaFoldDB

1 variants for P06839

Variant ID(s) Position Change Description Diseaes Association Provenance
s05-529015 647 R>C No SGRP

No associated diseases with P06839

1 regional properties for P06839

Type Name Position InterPro Accession
domain Glycosyl hydrolase family 59, central domain 332 - 400 IPR035394

Functions

Description
EC Number 3.6.4.12 Acting on ATP; involved in cellular and subcellular movement
Subcellular Localization
  • Nucleus
PANTHER Family
PANTHER Subfamily
PANTHER Protein Class
PANTHER Pathway Category No pathway information available

5 GO annotations of cellular component

Name Definition
cytosol The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
nucleotide-excision repair factor 3 complex One of several protein complexes involved in nucleotide-excision repair; possesses endodeoxynuclease and DNA helicase activities. In S. cerevisiae, it is composed of Rad2p and the core TFIIH-Ssl2p complex (core TFIIH is composed of Rad3p, Tfb1p, Tfb2p, Ssl1p, Tfb4p and Tfb5p. Note that Ssl2p is also called Rad25p).
nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
transcription factor TFIIH core complex The 7 subunit core of TFIIH that is a part of either the general transcription factor holo-TFIIH or the nucleotide-excision repair factor 3 complex. In S. cerevisiae/humans the complex is composed of: Ssl2/XPB, Tfb1/p62, Tfb2/p52, Ssl1/p44, Tfb4/p34, Tfb5/p8 and Rad3/XPD.
transcription factor TFIIH holo complex A complex that is capable of kinase activity directed towards the C-terminal Domain (CTD) of the largest subunit of RNA polymerase II and is essential for initiation at RNA polymerase II promoters in vitro. It is composed of the core TFIIH complex and the TFIIK complex.

8 GO annotations of molecular function

Name Definition
4 iron, 4 sulfur cluster binding Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
5'-3' DNA helicase activity Unwinding a DNA helix in the 5' to 3' direction, driven by ATP hydrolysis.
ATP binding Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
ATP hydrolysis activity Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
ATP-dependent activity, acting on DNA Catalytic activity that acts to modify DNA, driven by ATP hydrolysis.
damaged DNA binding Binding to damaged DNA.
DNA helicase activity Unwinding of a DNA helix, driven by ATP hydrolysis.
metal ion binding Binding to a metal ion.

9 GO annotations of biological process

Name Definition
nucleotide-excision repair A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
nucleotide-excision repair, DNA duplex unwinding The unwinding, or local denaturation, of the DNA duplex to create a bubble around the site of the DNA damage.
nucleotide-excision repair, DNA incision A process that results in the endonucleolytic cleavage of the damaged strand of DNA. The incision occurs at the junction of single-stranded DNA and double-stranded DNA that is formed when the DNA duplex is unwound.
phosphorylation of RNA polymerase II C-terminal domain The process of introducing a phosphate group on to an amino acid residue in the C-terminal domain of RNA polymerase II. Typically, this occurs during the transcription cycle and results in production of an RNA polymerase II enzyme where the carboxy-terminal domain (CTD) of the largest subunit is extensively phosphorylated, often referred to as hyperphosphorylated or the II(0) form. Specific types of phosphorylation within the CTD are usually associated with specific regions of genes, though there are exceptions. The phosphorylation state regulates the association of specific complexes such as the capping enzyme or 3'-RNA processing machinery to the elongating RNA polymerase complex.
positive regulation of mitotic recombination Any process that activates or increases the frequency, rate or extent of DNA recombination during mitosis.
regulation of mitotic recombination Any process that modulates the frequency, rate or extent of DNA recombination during mitosis.
regulation of transposition, RNA-mediated Any process that modulates the frequency, rate or extent of RNA-mediated transposition. RNA-mediated transposition is a type of transpositional recombination which occurs via an RNA intermediate.
transcription by RNA polymerase II The synthesis of RNA from a DNA template by RNA polymerase II (RNAP II), originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
transcription initiation at RNA polymerase II promoter A transcription initiation process that takes place at a RNA polymerase II gene promoter. Messenger RNAs (mRNA) genes, as well as some non-coding RNAs, are transcribed by RNA polymerase II.

3 homologous proteins in AiPD

UniProt AC Gene Name Protein Name Species Evidence Code
A6QLJ0 ERCC2 General transcription and DNA repair factor IIH helicase subunit XPD Bos taurus (Bovine) PR
P18074 ERCC2 General transcription and DNA repair factor IIH helicase subunit XPD Homo sapiens (Human) PR
O08811 Ercc2 General transcription and DNA repair factor IIH helicase subunit XPD Mus musculus (Mouse) PR
10 20 30 40 50 60
MKFYIDDLPV LFPYPKIYPE QYNYMCDIKK TLDVGGNSIL EMPSGTGKTV SLLSLTIAYQ
70 80 90 100 110 120
MHYPEHRKII YCSRTMSEIE KALVELENLM DYRTKELGYQ EDFRGLGLTS RKNLCLHPEV
130 140 150 160 170 180
SKERKGTVVD EKCRRMTNGQ AKRKLEEDPE ANVELCEYHE NLYNIEVEDY LPKGVFSFEK
190 200 210 220 230 240
LLKYCEEKTL CPYFIVRRMI SLCNIIIYSY HYLLDPKIAE RVSNEVSKDS IVIFDEAHNI
250 260 270 280 290 300
DNVCIESLSL DLTTDALRRA TRGANALDER ISEVRKVDSQ KLQDEYEKLV QGLHSADILT
310 320 330 340 350 360
DQEEPFVETP VLPQDLLTEA IPGNIRRAEH FVSFLKRLIE YLKTRMKVLH VISETPKSFL
370 380 390 400 410 420
QHLKQLTFIE RKPLRFCSER LSLLVRTLEV TEVEDFTALK DIATFATLIS TYEEGFLLII
430 440 450 460 470 480
EPYEIENAAV PNPIMRFTCL DASIAIKPVF ERFSSVIITS GTISPLDMYP RMLNFKTVLQ
490 500 510 520 530 540
KSYAMTLAKK SFLPMIITKG SDQVAISSRF EIRNDPSIVR NYGSMLVEFA KITPDGMVVF
550 560 570 580 590 600
FPSYLYMESI VSMWQTMGIL DEVWKHKLIL VETPDAQETS LALETYRKAC SNGRGAILLS
610 620 630 640 650 660
VARGKVSEGI DFDHQYGRTV LMIGIPFQYT ESRILKARLE FMRENYRIRE NDFLSFDAMR
670 680 690 700 710 720
HAAQCLGRVL RGKDDYGVMV LADRRFSRKR SQLPKWIAQG LSDADLNLST DMAISNTKQF
730 740 750 760 770
LRTMAQPTDP KDQEGVSVWS YEDLIKHQNS RKDQGGFIEN ENKEGEQDED EDEDIEMQ